We study genes of the rabbit immune system by techniques of molecular biology and immunology. Rabbits of the Alicia strain have a mutation (ali) that segregates with the immunoglobulin heavy chain (Igh) locus and has a cis effect upon the expression of heavy chain variable region genes (VH) encoding the a2 allotype. A relatively small deletion affects a segment containing 3'VH genes, the loss of which leads to the ali phenotype. The 3'end of the VH locus probably plays a key role in regulation of VH gene expression in rabbits because the VH1 gene is the target of preferential VDJ rearrangement. This raises the possibility that somatic mechanisms such as gene conversion and hypermutation make major contributions to generating the rabbit's antibody repertoire. DNAs from homozygous VH-CH recombinant rabbits and from the appropriate non-recombinant parental haplotypes were characterized using Southern blots hybridized with a panel of probes derived from cloned regions of the rabbit immunoglobulin heavy chain gene complex. In all three recombinants, the site was downstream of the entire VH cluster and upstream of the JH cluster within an about 50 kb region containing expanses of repetitive-sequence DNA as well as DH genes. The rabbit has two isotypic forms of the immunoglobulin kappa light chain, K1 and K2 which probably arose by duplication. In the normal rabbit, only traces of K2 light chains are produced. We used pulsed field and transverse alternating field electrophoresis to obtain megabase maps and found that the two Ckappa genes are about 1 megabase apart. One explanation for the poor expression of K2, could be great physical distance from Vkappa genes. However, we found that there are Vkappa, Jkappa and Ckappa2 genes within a about 105 kb fragment. Thus physical distance of Vkappa from Ckappa2 may not be the basis for poor K2 expression. We were interested in looking for second enhancers 3' of the Ckappa genes because the absence of a 3' enhancer in the K2 locus could explain the preferential utilization of the K1 isotype. A strong region of enhancer activity is found about 7 kb downstream of the Ckappa2 gene. Tbus absence of the 3' enhancer is probably not the explanation for low expression of the K2 gene.